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- PDB-4xsp: Crystal structure of Anabaena Alr3699/HepE in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 4xsp
TitleCrystal structure of Anabaena Alr3699/HepE in complex with UDP
ComponentsAlr3699 protein
KeywordsTRANSFERASE / GT-B fold / glycosyltransferase
Function / homology
Function and homology information


biosynthetic process / glycosyltransferase activity / nucleotide binding
Similarity search - Function
Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Alr3699 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWang, X.P. / Dai, Y.N. / Jiang, Y.L. / Cheng, W. / Chen, Y.X. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370757 China
CitationJournal: Glycobiology / Year: 2016
Title: Structural and enzymatic analyses of a glucosyltransferase Alr3699/HepE involved in Anabaena heterocyst envelop polysaccharide biosynthesis
Authors: Wang, X.P. / Jiang, Y.L. / Dai, Y.N. / Cheng, W. / Chen, Y. / Zhou, C.Z.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Alr3699 protein
A: Alr3699 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3355
Polymers84,7472
Non-polymers5883
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-25 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.883, 133.223, 143.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Alr3699 protein


Mass: 42373.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / UTEX 2576) (bacteria)
Strain: PCC 7120 / UTEX 2576 / Gene: alr3699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YQW3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.52 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0M ammonium citrate tribasic pH 7.0, 0.1M Bis-Tris propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 41058 / % possible obs: 99.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.16
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.48 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data scaling
MOLREPmodel building
HKL-2000data reduction
iMOSFLMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XSO

4xso


Resolution: 2.15→35.78 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.928 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24371 2054 5 %RANDOM
Rwork0.20584 ---
obs0.20776 38849 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.134 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20 Å2
2---1.34 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.15→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 37 152 5759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195709
X-RAY DIFFRACTIONr_bond_other_d0.0010.025593
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9627759
X-RAY DIFFRACTIONr_angle_other_deg0.757312813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5485725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16224.777247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24815941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1921528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021302
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6953.9842912
X-RAY DIFFRACTIONr_mcbond_other2.6913.9832911
X-RAY DIFFRACTIONr_mcangle_it3.8475.9623633
X-RAY DIFFRACTIONr_mcangle_other3.8475.9633634
X-RAY DIFFRACTIONr_scbond_it3.4134.4452797
X-RAY DIFFRACTIONr_scbond_other3.4124.4452797
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2826.5154127
X-RAY DIFFRACTIONr_long_range_B_refined6.79532.2646392
X-RAY DIFFRACTIONr_long_range_B_other6.80232.2376348
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 153 -
Rwork0.281 2767 -
obs--97.4 %

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